FormalGrammars: (Context-free) grammars in formal language theory

[ bioinformatics, formal-languages, gpl, library ] [ Propose Tags ]

Context-free grammars in formal language theory are sets of production rules, non-terminal and terminal symbols. This library provides basic data types and functions to manipulate such grammars.

Grammars can be defined in a small domain-specific language that is very close to typical CFG notation. The DSL parser can easily be extended. Grammar products, for example, are implemented as a single additional sub-parser.

This library also provides the machinery that transforms an Inside grammar into the corresponding Outside grammar.

In addition, TemplateHaskell and QuasiQuoting functionality allow embedding thusly defined grammars in Haskell programs. ADPfusion then turns such a grammar into an efficient dynamic program. It is also possible to generate Haskell modules that contain the resulting grammar, signature and algebra product.

Alternatives are ansi- or LaTeX-based pretty-printing for users that want to implement their CFG in another language than Haskell.

Formal background can be found in these papers:

Christian Hoener zu Siederdissen
Sneaking Around ConcatMap: Efficient Combinators for Dynamic Programming
2012. Proceedings of the 17th ACM SIGPLAN international conference on Functional programming preprint:
Andrew Farmer, Christian Höner zu Siederdissen, and Andy Gill.
The HERMIT in the stream: fusing stream fusion’s concatMap.
2014. Proceedings of the ACM SIGPLAN 2014 workshop on Partial evaluation and program manipulation.
Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler.
Product Grammars for Alignment and Folding.
2014. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 99.
Christian Höner zu Siederdissen, Sonja J. Prohaska, and Peter F. Stadler.
Algebraic Dynamic Programming over General Data Structures.
2015. submitted.

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Dependencies ADPfusion (>=0.4.0 && <0.4.1), ansi-wl-pprint (>=0.6.7 && <0.6.8), base (>=4.7 && <4.9), bytestring (>=0.10 && <0.11), cmdargs (>=0.10 && <0.11), containers, data-default (>=0.5 && <0.6), FormalGrammars, HaTeX (>=3.16 && <3.17), lens (>=4 && <5), mtl (>=2 && <3), parsers (>=0.12 && <0.13), PrimitiveArray (>=0.6.0 && <0.6.1), semigroups (>=0.16 && <0.17), template-haskell, text (>=1 && <2), transformers (>=0.3 && <0.5), trifecta (>=1.5 && <1.6), unordered-containers (>=0.2 && <0.3), vector (>=0.10 && <0.11) [details]
License GPL-3.0-only
Copyright Christian Hoener zu Siederdissen, 2013-2015
Author Christian Hoener zu Siederdissen, 2013-2015
Category Formal Languages, Bioinformatics
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Source repo head: git clone git://
Uploaded by ChristianHoener at 2015-05-07T15:04:58Z
Distributions NixOS:
Executables NeedlemanWunschFG, NussinovFG, GrammarPP
Downloads 8118 total (16 in the last 30 days)
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Status Docs available [build log]
Last success reported on 2015-05-07 [all 1 reports]

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